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I believe (I could be wrong) there are three small mistakes on lines `192`, `246` and `312` of `pubmed_oa_parser.py` in the `parse_references`, `parse_paragraph` and `parse_pubmed_caption` functions,…
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SupportingText (BEL 2.0, examples http://openbel.org/language/web/version_2.0/bel_specification_version_2.0.html) is not accepted instead of Evidence (BEL 1.0)
cebel updated
7 years ago
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here is one example that it gives error `Acta_Psychiatr_Scand/Acta_Psychiatr_Scand_2010_Feb_121(2)_152-156.nxml`. I'll update the issue soon.
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BioJS was initially a [registry of browser components for biological visualization](http://www.ebi.ac.uk/Tools/biojs/registry/). Bionode is more oriented for data manipulation (finding, parsing, analy…
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Using the latest vcf2db
Codon field (codon_change) is blank. I'm using VEP to annotate consequences.
```
$ gemini query -q 'select chrom, start, end, codon_change, aa_change from variants WHER…
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In both Pubmed Open Access and MEDLINE open access, when we parse abstract text. It mostly includes blank space and new line `\n`. We can preprocess that later using `nltk` whitespace tokenizer. Howev…
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`path_list = [folder for folder in fullpath if os.path.splitext(folder)[-1] == ('.nxml' or '.xml')]`
Is this code correct? `('.nsml', '.xml')` can only return `.nxml`, so basically it can not get the…
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References seem like a good source of information. Jason wrote regular expressions to extract references last semester, but I think we need a more developed tool. I will look into available extraction…
tsalo updated
7 years ago
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I think this was a HighWire requirement:
source code and source data for a figure was contained within the caption of that figure, but the figure supplement is not.
I have been playing with this and …
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I think we can speed up the parser a lot by parallelize this [L105](https://github.com/titipata/pubmed_parser/blob/master/pubmed_parser/medline_parser.py#L105)